Corynebacterium glutamicum is an important industrial producer of various amino acids with great potential for the production of other metabolites. The complete genome sequences of two C. glutamicum strains were determined and the use of genome-based approaches (transcriptomics, proteomics, metabolomics, and fluxomics) provided large amounts of data on the metabolism of this bacterium and its regulation. Many tools for genetic manipulations in C. glutamicum have been developed and used for the analysis of gene functions as well as for the construction and improvement of production strains. These tools include various types of plasmid vectors (cloning, promoter-probe, and expression vectors), DNA transfer methods, cloning heterologous genes, introducing protein secretion systems and gene replacement and genome rearrangement methods. Here we summarize the latest developments in the field of genetic engineering in C. glutamicum, give examples of the use of these new tools, and mention the challenges which stand in the way of fully implementing these tools and this acquired knowledge for the construction of superior production strains.